From 608c4f72a15b413f169692eb96630827411e37d4 Mon Sep 17 00:00:00 2001 From: FabianAicheler Date: Mon, 29 Oct 2018 17:03:29 +0100 Subject: [PATCH 1/3] Added Alignment Params (no logic) --- src/utils/MetabolomicsLFQ.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/utils/MetabolomicsLFQ.cpp b/src/utils/MetabolomicsLFQ.cpp index 69b2d67253e..a1419ec7005 100644 --- a/src/utils/MetabolomicsLFQ.cpp +++ b/src/utils/MetabolomicsLFQ.cpp @@ -54,6 +54,8 @@ #include +#include + #include //#include "FeatureLinkerBase.cpp" @@ -146,6 +148,11 @@ class UTILMetabolomicsLFQ : combined.insert("Identification_ams:", p_ams); combined.setSectionDescription("Identification_ams", "Accurate Mass Search parameters"); + //MapAligner pose + Param p_align = MapAlignmentAlgorithmPoseClustering().getParameters(); + combined.insert("Quantification_alignment:", p_align); + combined.setSectionDescription("Quantification_alignment", "Map Alignment parameters"); + //FL //do we set linking file explicitly? //registerOutputFile_("out_linking", "", "", "Output file", true); From 1daf2e6e13746203352557607384b1fbccfd2774 Mon Sep 17 00:00:00 2001 From: FabianAicheler Date: Mon, 29 Oct 2018 17:55:11 +0100 Subject: [PATCH 2/3] small reorder of parameters --- src/utils/MetabolomicsLFQ.cpp | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/utils/MetabolomicsLFQ.cpp b/src/utils/MetabolomicsLFQ.cpp index a1419ec7005..2e7fd31da52 100644 --- a/src/utils/MetabolomicsLFQ.cpp +++ b/src/utils/MetabolomicsLFQ.cpp @@ -139,15 +139,6 @@ class UTILMetabolomicsLFQ : //combined.insert("Linking:", fl_defaults); //combined.insert("AccurateMassSearch", ams_defaults); - //AMS - //currently no adduct files as parameter, use hardwiring? - //do we want out_annotation as optional file, or hardwire? - registerOutputFile_("out_annotation", "", "", "A copy of the input file, annotated with matching hits from the database.", false); - setValidFormats_("out_annotation", ListUtils::create("featureXML,consensusXML")); - Param p_ams = AccurateMassSearchEngine().getDefaults(); - combined.insert("Identification_ams:", p_ams); - combined.setSectionDescription("Identification_ams", "Accurate Mass Search parameters"); - //MapAligner pose Param p_align = MapAlignmentAlgorithmPoseClustering().getParameters(); combined.insert("Quantification_alignment:", p_align); @@ -164,6 +155,15 @@ class UTILMetabolomicsLFQ : //Do we want to allow the keep_subelements' option or hardwire to false? (true returns ONLY the subelements I think, no consensus. Or something like that, have to evaluate use case.) //registerFlag_("keep_subelements", "For consensusXML input only: If set, the sub-features of the inputs are transferred to the output."); + //AMS + //currently no adduct files as parameter, use hardwiring? + //do we want out_annotation as optional file, or hardwire? + registerOutputFile_("out_annotation", "", "", "A copy of the input file, annotated with matching hits from the database.", false); + setValidFormats_("out_annotation", ListUtils::create("featureXML,consensusXML")); + Param p_ams = AccurateMassSearchEngine().getDefaults(); + combined.insert("Identification_ams:", p_ams); + combined.setSectionDescription("Identification_ams", "Accurate Mass Search parameters"); + registerFullParam_(combined); } From bb53ae52ec9747fb946f2667d485d194544de05f Mon Sep 17 00:00:00 2001 From: FabianAicheler Date: Mon, 29 Oct 2018 18:15:30 +0100 Subject: [PATCH 3/3] connect main body alignment Params to dialog --- src/utils/MetabolomicsLFQ.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/utils/MetabolomicsLFQ.cpp b/src/utils/MetabolomicsLFQ.cpp index 2e7fd31da52..ba4870e63f9 100644 --- a/src/utils/MetabolomicsLFQ.cpp +++ b/src/utils/MetabolomicsLFQ.cpp @@ -242,9 +242,9 @@ class UTILMetabolomicsLFQ : writeDebug_("Parameters passed to FeatureFindingMetabo", ffm_param, 3); // Parameter for MapAlignPoseClustering + Param ma_param = getParam_().copy("Quantification_alignment:", true); + writeDebug_("Parameters passed to MapAlignerPoseClustering", ma_param, 3); /* - Param ma_param = getParam_().copy("Alignment:", true); - writeDebug_("Parameters passed to MapAlignmentPoseClustering algorithm", ma_param, 3); MapAlignmentPoseClustering ma; ma.setLogType(log_type_); ma.setParameters(ff_param);